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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.7

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2019-10-25, 11:19 based on data in: /media/wei/My Passport/Work_data_sheep_arc/BBSRC_SHEEP/fastqc_trimmed_report_biopsy


        General Statistics

        Showing 360/360 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        trimmed_6565g1w1_S3_R1_001
        46.6%
        50%
        24.8
        trimmed_6565g1w1_S3_R2_001
        39.9%
        51%
        24.8
        trimmed_6565g1w2_S2_R1_001
        54.8%
        50%
        30.1
        trimmed_6565g1w2_S2_R2_001
        48.4%
        51%
        30.1
        trimmed_6565g1w3_S16_R1_001
        35.2%
        50%
        23.7
        trimmed_6565g1w3_S16_R2_001
        32.9%
        51%
        23.7
        trimmed_6565g1w4_S1_R1_001
        34.1%
        50%
        20.1
        trimmed_6565g1w4_S1_R2_001
        31.9%
        51%
        20.1
        trimmed_6565g1w5_S2_R1_001
        46.3%
        52%
        19.2
        trimmed_6565g1w5_S2_R2_001
        43.6%
        52%
        19.2
        trimmed_6565g1w7_S14_R1_001
        50.6%
        51%
        26.8
        trimmed_6565g1w7_S14_R2_001
        45.5%
        52%
        26.8
        trimmed_6576g3w1_S8_R1_001
        47.0%
        52%
        26.7
        trimmed_6576g3w1_S8_R2_001
        44.2%
        52%
        26.7
        trimmed_6576g3w2_S9_S13_R1_001
        38.4%
        51%
        34.8
        trimmed_6576g3w2_S9_S13_R2_001
        33.5%
        51%
        34.8
        trimmed_6576g3w3_S3_R1_001
        45.7%
        49%
        27.3
        trimmed_6576g3w3_S3_R2_001
        43.7%
        50%
        27.3
        trimmed_6576g3w4_S5_R1_001
        48.4%
        50%
        27.6
        trimmed_6576g3w4_S5_R2_001
        46.9%
        51%
        27.6
        trimmed_6576g3w5_S9_R1_001
        49.3%
        50%
        28.1
        trimmed_6576g3w5_S9_R2_001
        47.9%
        51%
        28.1
        trimmed_6576g3w7_S2_R1_001
        49.9%
        52%
        19.6
        trimmed_6576g3w7_S2_R2_001
        47.2%
        53%
        19.6
        trimmed_6588g2w1_S5_R1_001
        36.0%
        50%
        26.5
        trimmed_6588g2w1_S5_R2_001
        35.3%
        50%
        26.5
        trimmed_6588g2w2_S7_R1_001
        47.8%
        51%
        25.8
        trimmed_6588g2w2_S7_R2_001
        44.8%
        51%
        25.8
        trimmed_6588g2w3_S19_R1_001
        46.3%
        52%
        20.0
        trimmed_6588g2w3_S19_R2_001
        44.1%
        52%
        20.0
        trimmed_6588g2w4_S22_R1_001
        47.1%
        51%
        21.7
        trimmed_6588g2w4_S22_R2_001
        44.5%
        52%
        21.7
        trimmed_6588g2w5_S14_R1_001
        47.4%
        53%
        26.6
        trimmed_6588g2w5_S14_R2_001
        45.8%
        53%
        26.6
        trimmed_6588g2w7_S10_R1_001
        43.6%
        52%
        23.1
        trimmed_6588g2w7_S10_R2_001
        41.2%
        52%
        23.1
        trimmed_6595g4w1_S10_R1_001
        47.8%
        50%
        30.9
        trimmed_6595g4w1_S10_R2_001
        45.7%
        51%
        30.9
        trimmed_6595g4w2_S1_R1_001
        46.9%
        50%
        29.5
        trimmed_6595g4w2_S1_R2_001
        45.7%
        51%
        29.5
        trimmed_6595g4w3_S4_R1_001
        52.7%
        51%
        28.4
        trimmed_6595g4w3_S4_R2_001
        46.1%
        51%
        28.4
        trimmed_6595g4w4_S15_R1_001
        48.2%
        51%
        18.2
        trimmed_6595g4w4_S15_R2_001
        46.2%
        52%
        18.2
        trimmed_6595g4w5_S13_R1_001
        47.6%
        51%
        25.4
        trimmed_6595g4w5_S13_R2_001
        43.9%
        52%
        25.4
        trimmed_6595g4w7_S7_R1_001
        50.5%
        52%
        22.1
        trimmed_6595g4w7_S7_R2_001
        50.5%
        53%
        22.1
        trimmed_6615g1w1_S3_R1_001
        53.3%
        51%
        27.4
        trimmed_6615g1w1_S3_R2_001
        49.8%
        52%
        27.4
        trimmed_6615g1w2_S22_R1_001
        43.3%
        50%
        28.3
        trimmed_6615g1w2_S22_R2_001
        39.1%
        50%
        28.3
        trimmed_6615g1w3_S16_R1_001
        48.2%
        50%
        23.9
        trimmed_6615g1w3_S16_R2_001
        45.5%
        51%
        23.9
        trimmed_6615g1w4_S9_R1_001
        49.9%
        52%
        29.7
        trimmed_6615g1w4_S9_R2_001
        46.5%
        52%
        29.7
        trimmed_6615g1w5_S12_R1_001
        44.0%
        51%
        20.5
        trimmed_6615g1w5_S12_R2_001
        40.1%
        51%
        20.5
        trimmed_6615g1w7_S13_R1_001
        47.4%
        53%
        24.6
        trimmed_6615g1w7_S13_R2_001
        46.9%
        53%
        24.6
        trimmed_6622g1w1_S1_R1_001
        45.2%
        50%
        21.3
        trimmed_6622g1w1_S1_R2_001
        41.9%
        50%
        21.3
        trimmed_6622g1w2_S4_R1_001
        49.5%
        51%
        28.2
        trimmed_6622g1w2_S4_R2_001
        45.0%
        51%
        28.2
        trimmed_6622g1w3_S8_R1_001
        50.7%
        49%
        31.3
        trimmed_6622g1w3_S8_R2_001
        47.5%
        49%
        31.3
        trimmed_6622g1w4_S8_R1_001
        50.3%
        51%
        30.3
        trimmed_6622g1w4_S8_R2_001
        44.1%
        51%
        30.3
        trimmed_6622g1w5_S17_R1_001
        36.7%
        49%
        22.6
        trimmed_6622g1w5_S17_R2_001
        34.7%
        50%
        22.6
        trimmed_6622g1w7_S9_R1_001
        49.2%
        50%
        34.9
        trimmed_6622g1w7_S9_R2_001
        46.9%
        51%
        34.9
        trimmed_6625g2w1_S16_R1_001
        42.5%
        50%
        32.0
        trimmed_6625g2w1_S16_R2_001
        37.2%
        50%
        32.0
        trimmed_6625g2w2_S10_R1_001
        46.2%
        52%
        22.6
        trimmed_6625g2w2_S10_R2_001
        43.8%
        52%
        22.6
        trimmed_6625g2w3_S20_R1_001
        40.1%
        49%
        25.0
        trimmed_6625g2w3_S20_R2_001
        34.3%
        50%
        25.0
        trimmed_6625g2w4_S2_R1_001
        47.5%
        52%
        23.8
        trimmed_6625g2w4_S2_R2_001
        45.3%
        53%
        23.8
        trimmed_6625g2w5_S8_R1_001
        46.5%
        52%
        21.1
        trimmed_6625g2w5_S8_R2_001
        44.1%
        52%
        21.1
        trimmed_6625g2w7_S17_R1_001
        48.5%
        50%
        31.3
        trimmed_6625g2w7_S17_R2_001
        44.5%
        50%
        31.3
        trimmed_6626g2w1_S7_R1_001
        49.0%
        51%
        22.8
        trimmed_6626g2w1_S7_R2_001
        46.2%
        51%
        22.8
        trimmed_6626g2w2_S6_R1_001
        35.6%
        50%
        25.4
        trimmed_6626g2w2_S6_R2_001
        33.8%
        50%
        25.4
        trimmed_6626g2w3_S6_R1_001
        51.0%
        50%
        34.9
        trimmed_6626g2w3_S6_R2_001
        43.8%
        51%
        34.9
        trimmed_6626g2w4_S5_R1_001
        46.5%
        52%
        22.4
        trimmed_6626g2w4_S5_R2_001
        43.0%
        52%
        22.4
        trimmed_6626g2w5_S12_R1_001
        46.6%
        50%
        25.3
        trimmed_6626g2w5_S12_R2_001
        42.1%
        51%
        25.3
        trimmed_6626g2w7_S17_R1_001
        46.0%
        51%
        22.6
        trimmed_6626g2w7_S17_R2_001
        44.4%
        52%
        22.6
        trimmed_6634g2w1_S10_R1_001
        41.1%
        49%
        28.1
        trimmed_6634g2w1_S10_R2_001
        35.9%
        50%
        28.1
        trimmed_6634g2w2_S16_R1_001
        46.1%
        50%
        24.2
        trimmed_6634g2w2_S16_R2_001
        43.6%
        51%
        24.2
        trimmed_6634g2w3_S19_R1_001
        44.4%
        51%
        24.7
        trimmed_6634g2w3_S19_R2_001
        41.4%
        51%
        24.7
        trimmed_6634g2w4_S5_R1_001
        44.4%
        53%
        25.7
        trimmed_6634g2w4_S5_R2_001
        42.7%
        53%
        25.7
        trimmed_6634g2w5_S3_R1_001
        52.9%
        50%
        33.4
        trimmed_6634g2w5_S3_R2_001
        46.1%
        51%
        33.4
        trimmed_6634g2w7_S20_R1_001
        45.0%
        52%
        24.1
        trimmed_6634g2w7_S20_R2_001
        42.5%
        52%
        24.1
        trimmed_6635g4w1_S3_R1_001
        45.0%
        51%
        19.8
        trimmed_6635g4w1_S3_R2_001
        40.9%
        52%
        19.8
        trimmed_6635g4w2_S12_R1_001
        45.9%
        53%
        18.5
        trimmed_6635g4w2_S12_R2_001
        44.4%
        53%
        18.5
        trimmed_6635g4w3_S21_R1_001
        47.1%
        52%
        19.5
        trimmed_6635g4w3_S21_R2_001
        45.4%
        53%
        19.5
        trimmed_6635g4w4_S22_R1_001
        47.4%
        52%
        25.0
        trimmed_6635g4w4_S22_R2_001
        44.7%
        53%
        25.0
        trimmed_6635g4w5_S1_R1_001
        47.7%
        51%
        20.4
        trimmed_6635g4w5_S1_R2_001
        43.9%
        52%
        20.4
        trimmed_6635g4w7_S13_R1_001
        48.2%
        51%
        27.3
        trimmed_6635g4w7_S13_R2_001
        46.8%
        51%
        27.3
        trimmed_6639g4w1_S16_R1_001
        46.0%
        52%
        22.5
        trimmed_6639g4w1_S16_R2_001
        44.1%
        53%
        22.5
        trimmed_6639g4w2_S2_R1_001
        46.2%
        50%
        27.0
        trimmed_6639g4w2_S2_R2_001
        42.3%
        51%
        27.0
        trimmed_6639g4w3_S4_R1_001
        45.6%
        53%
        19.6
        trimmed_6639g4w3_S4_R2_001
        43.1%
        53%
        19.6
        trimmed_6639g4w4_S7_R1_001
        48.3%
        51%
        27.1
        trimmed_6639g4w4_S7_R2_001
        46.9%
        51%
        27.1
        trimmed_6639g4w5_S10_R1_001
        47.7%
        50%
        25.6
        trimmed_6639g4w5_S10_R2_001
        46.0%
        51%
        25.6
        trimmed_6639g4w7_S6_R1_001
        47.8%
        53%
        22.0
        trimmed_6639g4w7_S6_R2_001
        45.8%
        53%
        22.0
        trimmed_6642g1w1_S4_R1_001
        48.3%
        52%
        19.6
        trimmed_6642g1w1_S4_R2_001
        46.0%
        53%
        19.6
        trimmed_6642g1w2_S13_R1_001
        49.0%
        51%
        24.6
        trimmed_6642g1w2_S13_R2_001
        46.2%
        51%
        24.6
        trimmed_6642g1w3_S3_R1_001
        48.5%
        50%
        29.4
        trimmed_6642g1w3_S3_R2_001
        44.6%
        51%
        29.4
        trimmed_6642g1w4_S5_R1_001
        50.6%
        50%
        31.2
        trimmed_6642g1w4_S5_R2_001
        48.0%
        51%
        31.2
        trimmed_6642g1w5_S5_R1_001
        47.5%
        52%
        21.4
        trimmed_6642g1w5_S5_R2_001
        44.8%
        52%
        21.4
        trimmed_6642g1w7_S15_R1_001
        47.7%
        50%
        28.3
        trimmed_6642g1w7_S15_R2_001
        43.5%
        51%
        28.3
        trimmed_6647g3w1_S9_R1_001
        41.2%
        50%
        28.2
        trimmed_6647g3w1_S9_R2_001
        37.0%
        51%
        28.2
        trimmed_6647g3w2_S12_R1_001
        47.2%
        51%
        27.4
        trimmed_6647g3w2_S12_R2_001
        45.9%
        52%
        27.4
        trimmed_6647g3w3_S4_R1_001
        45.2%
        50%
        25.9
        trimmed_6647g3w3_S4_R2_001
        43.0%
        51%
        25.9
        trimmed_6647g3w4_S1_R1_001
        45.9%
        52%
        13.4
        trimmed_6647g3w4_S1_R2_001
        43.7%
        53%
        13.4
        trimmed_6647g3w5_S4_R1_001
        49.9%
        53%
        15.8
        trimmed_6647g3w5_S4_R2_001
        47.0%
        54%
        15.8
        trimmed_6647g3w7_S2_R1_001
        44.7%
        53%
        18.3
        trimmed_6647g3w7_S2_R2_001
        42.3%
        53%
        18.3
        trimmed_6652g3w1_S22_R1_001
        35.6%
        50%
        24.4
        trimmed_6652g3w1_S22_R2_001
        34.2%
        50%
        24.4
        trimmed_6652g3w2_S3_R1_001
        53.3%
        50%
        37.8
        trimmed_6652g3w2_S3_R2_001
        45.3%
        51%
        37.8
        trimmed_6652g3w3_S1_R1_001
        49.8%
        52%
        26.9
        trimmed_6652g3w3_S1_R2_001
        48.0%
        52%
        26.9
        trimmed_6652g3w4_S6_R1_001
        50.9%
        50%
        27.8
        trimmed_6652g3w4_S6_R2_001
        50.0%
        50%
        27.8
        trimmed_6652g3w5_S7_R1_001
        40.4%
        52%
        10.3
        trimmed_6652g3w5_S7_R2_001
        38.3%
        52%
        10.3
        trimmed_6652g3w7_S2_R1_001
        50.2%
        52%
        22.7
        trimmed_6652g3w7_S2_R2_001
        47.3%
        52%
        22.7
        trimmed_6653g4w1_S19_R1_001
        48.2%
        51%
        26.3
        trimmed_6653g4w1_S19_R2_001
        46.1%
        51%
        26.3
        trimmed_6653g4w2_S8_R1_001
        47.8%
        51%
        23.9
        trimmed_6653g4w2_S8_R2_001
        45.8%
        52%
        23.9
        trimmed_6653g4w3_S24_R1_001
        49.8%
        52%
        19.9
        trimmed_6653g4w3_S24_R2_001
        47.2%
        53%
        19.9
        trimmed_6653g4w4_S19_R1_001
        43.6%
        50%
        26.5
        trimmed_6653g4w4_S19_R2_001
        39.2%
        51%
        26.5
        trimmed_6653g4w5_S1_R1_001
        42.5%
        52%
        16.2
        trimmed_6653g4w5_S1_R2_001
        39.9%
        53%
        16.2
        trimmed_6653g4w7_S14_R1_001
        49.3%
        49%
        28.0
        trimmed_6653g4w7_S14_R2_001
        48.0%
        50%
        28.0
        trimmed_6902g4w1_S2_R1_001
        48.6%
        50%
        25.2
        trimmed_6902g4w1_S2_R2_001
        43.0%
        51%
        25.2
        trimmed_6902g4w2_S15_R1_001
        48.1%
        53%
        20.2
        trimmed_6902g4w2_S15_R2_001
        46.2%
        53%
        20.2
        trimmed_6902g4w3_S15_R1_001
        48.8%
        52%
        25.2
        trimmed_6902g4w3_S15_R2_001
        46.8%
        53%
        25.2
        trimmed_6902g4w4_S5_R1_001
        54.5%
        51%
        32.0
        trimmed_6902g4w4_S5_R2_001
        46.9%
        51%
        32.0
        trimmed_6902g4w5_S3_R1_001
        39.3%
        50%
        27.4
        trimmed_6902g4w5_S3_R2_001
        38.5%
        50%
        27.4
        trimmed_6902g4w7_S19_R1_001
        49.2%
        51%
        21.3
        trimmed_6902g4w7_S19_R2_001
        45.1%
        52%
        21.3
        trimmed_6905g3w1_S6_R1_001
        47.0%
        53%
        18.5
        trimmed_6905g3w1_S6_R2_001
        45.5%
        53%
        18.5
        trimmed_6905g3w2_S14_R1_001
        46.9%
        52%
        24.4
        trimmed_6905g3w2_S14_R2_001
        44.9%
        53%
        24.4
        trimmed_6905g3w3_S14_R1_001
        48.9%
        51%
        30.5
        trimmed_6905g3w3_S14_R2_001
        47.0%
        51%
        30.5
        trimmed_6905g3w4_S9_R1_001
        49.7%
        52%
        23.9
        trimmed_6905g3w4_S9_R2_001
        47.0%
        53%
        23.9
        trimmed_6905g3w5_S10_R1_001
        53.7%
        51%
        28.7
        trimmed_6905g3w5_S10_R2_001
        47.3%
        52%
        28.7
        trimmed_6905g3w7_S12_R1_001
        49.1%
        50%
        26.2
        trimmed_6905g3w7_S12_R2_001
        47.8%
        51%
        26.2
        trimmed_6910g3w1_S21_R1_001
        45.9%
        52%
        23.8
        trimmed_6910g3w1_S21_R2_001
        43.9%
        53%
        23.8
        trimmed_6910g3w2_S24_R1_001
        47.0%
        52%
        24.5
        trimmed_6910g3w2_S24_R2_001
        44.1%
        52%
        24.5
        trimmed_6910g3w3_S6_R1_001
        47.9%
        52%
        24.6
        trimmed_6910g3w3_S6_R2_001
        44.3%
        52%
        24.6
        trimmed_6910g3w4_S11_R1_001
        40.4%
        49%
        24.7
        trimmed_6910g3w4_S11_R2_001
        37.1%
        50%
        24.7
        trimmed_6910g3w5_S19_R1_001
        51.2%
        51%
        24.8
        trimmed_6910g3w5_S19_R2_001
        49.0%
        52%
        24.8
        trimmed_6910g3w7_S5_R1_001
        48.6%
        52%
        20.4
        trimmed_6910g3w7_S5_R2_001
        45.5%
        53%
        20.4
        trimmed_6911g3w1_S9_R1_001
        46.5%
        52%
        20.0
        trimmed_6911g3w1_S9_R2_001
        44.9%
        53%
        20.0
        trimmed_6911g3w2_S2_R1_001
        48.3%
        52%
        24.5
        trimmed_6911g3w2_S2_R2_001
        46.5%
        52%
        24.5
        trimmed_6911g3w3_S4_R1_001
        49.3%
        51%
        26.9
        trimmed_6911g3w3_S4_R2_001
        47.4%
        52%
        26.9
        trimmed_6911g3w4_S12_R1_001
        46.1%
        50%
        21.5
        trimmed_6911g3w4_S12_R2_001
        42.0%
        50%
        21.5
        trimmed_6911g3w5_S21_R1_001
        47.9%
        52%
        21.4
        trimmed_6911g3w5_S21_R2_001
        44.8%
        53%
        21.4
        trimmed_6911g3w7_S8_R1_001
        45.4%
        52%
        20.1
        trimmed_6911g3w7_S8_R2_001
        42.5%
        53%
        20.1
        trimmed_6915g2w1_S23_R1_001
        47.7%
        52%
        27.8
        trimmed_6915g2w1_S23_R2_001
        45.4%
        52%
        27.8
        trimmed_6915g2w2_S6_R1_001
        50.1%
        50%
        30.2
        trimmed_6915g2w2_S6_R2_001
        45.5%
        51%
        30.2
        trimmed_6915g2w3_S6_R1_001
        49.1%
        51%
        27.4
        trimmed_6915g2w3_S6_R2_001
        43.7%
        52%
        27.4
        trimmed_6915g2w4_S7_R1_001
        37.0%
        50%
        26.9
        trimmed_6915g2w4_S7_R2_001
        35.8%
        51%
        26.9
        trimmed_6915g2w5_S7_R1_001
        49.9%
        51%
        27.5
        trimmed_6915g2w5_S7_R2_001
        42.7%
        51%
        27.5
        trimmed_6915g2w7_S11_R1_001
        47.0%
        52%
        20.2
        trimmed_6915g2w7_S11_R2_001
        44.5%
        52%
        20.2
        trimmed_6917g1w1_S5_R1_001
        52.6%
        51%
        33.2
        trimmed_6917g1w1_S5_R2_001
        45.5%
        52%
        33.2
        trimmed_6917g1w2_S4_R1_001
        47.0%
        51%
        19.5
        trimmed_6917g1w2_S4_R2_001
        44.2%
        52%
        19.5
        trimmed_6917g1w3_S9_R1_001
        50.1%
        51%
        28.3
        trimmed_6917g1w3_S9_R2_001
        45.6%
        51%
        28.3
        trimmed_6917g1w4_S22_R1_001
        47.8%
        52%
        22.4
        trimmed_6917g1w4_S22_R2_001
        45.0%
        52%
        22.4
        trimmed_6917g1w5_S10_R1_001
        49.6%
        50%
        30.1
        trimmed_6917g1w5_S10_R2_001
        45.1%
        51%
        30.1
        trimmed_6917g1w7_S12_R1_001
        45.2%
        52%
        25.9
        trimmed_6917g1w7_S12_R2_001
        40.3%
        53%
        25.9
        trimmed_6923g4w1_S20_R1_001
        45.1%
        50%
        23.9
        trimmed_6923g4w1_S20_R2_001
        42.2%
        50%
        23.9
        trimmed_6923g4w2_S18_R1_001
        50.2%
        52%
        23.5
        trimmed_6923g4w2_S18_R2_001
        48.3%
        52%
        23.5
        trimmed_6923g4w3_S7_R1_001
        44.8%
        52%
        19.8
        trimmed_6923g4w3_S7_R2_001
        42.5%
        53%
        19.8
        trimmed_6923g4w4_S8_R1_001
        48.4%
        50%
        28.7
        trimmed_6923g4w4_S8_R2_001
        46.8%
        51%
        28.7
        trimmed_6923g4w5_S4_R1_001
        50.9%
        52%
        25.7
        trimmed_6923g4w5_S4_R2_001
        49.8%
        53%
        25.7
        trimmed_6923g4w7_S5_R1_001
        47.9%
        51%
        21.4
        trimmed_6923g4w7_S5_R2_001
        44.8%
        52%
        21.4
        trimmed_6925g1w1_S1_R1_001
        45.7%
        52%
        18.1
        trimmed_6925g1w1_S1_R2_001
        43.1%
        52%
        18.1
        trimmed_6925g1w2_S11_R1_001
        48.2%
        51%
        28.6
        trimmed_6925g1w2_S11_R2_001
        43.6%
        52%
        28.6
        trimmed_6925g1w3_S13_R1_001
        47.5%
        50%
        28.7
        trimmed_6925g1w3_S13_R2_001
        44.1%
        51%
        28.7
        trimmed_6925g1w4_S10_R1_001
        50.2%
        51%
        26.8
        trimmed_6925g1w4_S10_R2_001
        47.4%
        52%
        26.8
        trimmed_6925g1w5_S12_R1_001
        45.2%
        49%
        34.3
        trimmed_6925g1w5_S12_R2_001
        39.1%
        49%
        34.3
        trimmed_6925g1w7_S15_R1_001
        45.5%
        51%
        24.6
        trimmed_6925g1w7_S15_R2_001
        42.0%
        52%
        24.6
        trimmed_6928g3w1_S9_R1_001
        52.6%
        50%
        33.6
        trimmed_6928g3w1_S9_R2_001
        46.2%
        51%
        33.6
        trimmed_6928g3w2_S18_R1_001
        45.2%
        51%
        23.3
        trimmed_6928g3w2_S18_R2_001
        40.2%
        51%
        23.3
        trimmed_6928g3w3_S8_R1_001
        46.2%
        51%
        21.6
        trimmed_6928g3w3_S8_R2_001
        40.6%
        52%
        21.6
        trimmed_6928g3w4_S4_R1_001
        46.5%
        50%
        22.8
        trimmed_6928g3w4_S4_R2_001
        42.5%
        51%
        22.8
        trimmed_6928g3w5_S12_R1_001
        48.8%
        52%
        23.9
        trimmed_6928g3w5_S12_R2_001
        48.5%
        53%
        23.9
        trimmed_6928g3w7_S1_R1_001
        61.5%
        50%
        45.3
        trimmed_6928g3w7_S1_R2_001
        53.0%
        51%
        45.3
        trimmed_6931g2w1_S4_R1_001
        49.4%
        50%
        30.9
        trimmed_6931g2w1_S4_R2_001
        45.6%
        50%
        30.9
        trimmed_6931g2w2_S8_R1_001
        49.9%
        51%
        29.0
        trimmed_6931g2w2_S8_R2_001
        41.8%
        52%
        29.0
        trimmed_6931g2w3_S8_R1_001
        49.1%
        51%
        31.2
        trimmed_6931g2w3_S8_R2_001
        43.7%
        52%
        31.2
        trimmed_6931g2w4_S8_R1_001
        45.8%
        51%
        22.7
        trimmed_6931g2w4_S8_R2_001
        43.8%
        52%
        22.7
        trimmed_6931g2w5_S11_R1_001
        51.9%
        51%
        33.6
        trimmed_6931g2w5_S11_R2_001
        50.4%
        51%
        33.6
        trimmed_6931g2w7_S10_R1_001
        38.8%
        49%
        25.8
        trimmed_6931g2w7_S10_R2_001
        37.1%
        50%
        25.8
        trimmed_6934g4w1_S11_R1_001
        48.2%
        52%
        23.9
        trimmed_6934g4w1_S11_R2_001
        46.9%
        53%
        23.9
        trimmed_6934g4w2_S1_R1_001
        46.9%
        52%
        24.8
        trimmed_6934g4w2_S1_R2_001
        44.4%
        53%
        24.8
        trimmed_6934g4w3_S10_R1_001
        46.6%
        51%
        23.9
        trimmed_6934g4w3_S10_R2_001
        43.1%
        52%
        23.9
        trimmed_6934g4w4_S4_R1_001
        48.2%
        51%
        23.8
        trimmed_6934g4w4_S4_R2_001
        42.1%
        52%
        23.8
        trimmed_6934g4w5_S11_R1_001
        47.6%
        50%
        27.7
        trimmed_6934g4w5_S11_R2_001
        46.1%
        51%
        27.7
        trimmed_6934g4w7_S4_R1_001
        40.6%
        50%
        27.6
        trimmed_6934g4w7_S4_R2_001
        39.3%
        51%
        27.6
        trimmed_6935g2w1_S10_R1_001
        46.6%
        51%
        21.4
        trimmed_6935g2w1_S10_R2_001
        43.7%
        52%
        21.4
        trimmed_6935g2w2_S13_R1_001
        51.1%
        51%
        25.7
        trimmed_6935g2w2_S13_R2_001
        48.2%
        52%
        25.7
        trimmed_6935g2w3_S16_R1_001
        48.8%
        52%
        25.5
        trimmed_6935g2w3_S16_R2_001
        46.4%
        52%
        25.5
        trimmed_6935g2w4_S16_R1_001
        45.9%
        51%
        23.2
        trimmed_6935g2w4_S16_R2_001
        41.3%
        51%
        23.2
        trimmed_6935g2w5_S13_R1_001
        48.5%
        50%
        28.4
        trimmed_6935g2w5_S13_R2_001
        44.5%
        50%
        28.4
        trimmed_6935g2w7_S18_R1_001
        50.5%
        50%
        31.6
        trimmed_6935g2w7_S18_R2_001
        46.1%
        51%
        31.6
        trimmed_6937g1w1_S6_R1_001
        55.0%
        50%
        38.7
        trimmed_6937g1w1_S6_R2_001
        47.4%
        51%
        38.7
        trimmed_6937g1w2_S5_R1_001
        49.5%
        51%
        29.3
        trimmed_6937g1w2_S5_R2_001
        45.8%
        51%
        29.3
        trimmed_6937g1w3_S7_R1_001
        48.2%
        52%
        24.7
        trimmed_6937g1w3_S7_R2_001
        45.2%
        53%
        24.7
        trimmed_6937g1w4_S6_R1_001
        43.6%
        51%
        22.5
        trimmed_6937g1w4_S6_R2_001
        39.0%
        51%
        22.5
        trimmed_6937g1w5_S11_R1_001
        46.4%
        50%
        27.0
        trimmed_6937g1w5_S11_R2_001
        42.5%
        51%
        27.0
        trimmed_6937g1w7_S16_R1_001
        47.9%
        49%
        28.9
        trimmed_6937g1w7_S16_R2_001
        44.0%
        49%
        28.9
        trimmed_6939g4w1_S9_R1_001
        48.3%
        52%
        25.7
        trimmed_6939g4w1_S9_R2_001
        46.6%
        52%
        25.7
        trimmed_6939g4w2_S21_R1_001
        41.2%
        50%
        25.6
        trimmed_6939g4w2_S21_R2_001
        36.1%
        51%
        25.6
        trimmed_6939g4w3_S9_R1_001
        37.4%
        50%
        27.7
        trimmed_6939g4w3_S9_R2_001
        36.7%
        51%
        27.7
        trimmed_6939g4w4_S18_R1_001
        47.1%
        52%
        20.9
        trimmed_6939g4w4_S18_R2_001
        44.4%
        53%
        20.9
        trimmed_6939g4w5_S17_R1_001
        51.3%
        53%
        23.9
        trimmed_6939g4w5_S17_R2_001
        49.7%
        53%
        23.9
        trimmed_6939g4w7_S1_R1_001
        42.8%
        52%
        15.0
        trimmed_6939g4w7_S1_R2_001
        41.1%
        53%
        15.0
        trimmed_6940g2w1_S1_R1_001
        45.9%
        49%
        20.7
        trimmed_6940g2w1_S1_R2_001
        40.0%
        49%
        20.7
        trimmed_6940g2w2_S7_R1_001
        51.6%
        50%
        33.7
        trimmed_6940g2w2_S7_R2_001
        47.4%
        50%
        33.7
        trimmed_6940g2w3_S17_R1_001
        41.7%
        49%
        29.9
        trimmed_6940g2w3_S17_R2_001
        35.7%
        50%
        29.9
        trimmed_6940g2w4_S11_R1_001
        45.3%
        52%
        22.7
        trimmed_6940g2w4_S11_R2_001
        42.8%
        52%
        22.7
        trimmed_6940g2w5_S10_R1_001
        48.9%
        52%
        22.9
        trimmed_6940g2w5_S10_R2_001
        45.7%
        53%
        22.9
        trimmed_6940g2w7_S1_R1_001
        48.8%
        50%
        27.4
        trimmed_6940g2w7_S1_R2_001
        44.3%
        51%
        27.4

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        360 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%